15-78849442-T-C

Variant names:

• chr15-78849442-T-C
• rs7173743
• ENST00000379535.8:c.115+8767T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000379535.8(MORF4L1):​c.115+8767T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,180 control chromosomes in the GnomAD database, including 15,562 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.45 (15562 hom., cov: 29)
• Consequence: MORF4L1 ENST00000379535.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.67

Genes affected

MORF4L1 (HGNC:16989): (mortality factor 4 like 1) Enables protein N-terminus binding activity. Involved in double-strand break repair via homologous recombination and histone modification. Located in nuclear speck. Part of NuA4 histone acetyltransferase complex and Sin3 complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MORF4L1	ENST00000379535.8	c.115+8767T>C		intron_variant	Intron 2 of 12	2		ENSP00000368850.4
MORF4L1	ENST00000559697.5	n.415+1361T>C		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68024 AN: 151062 Hom.: 15547 Cov.: 29

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.475

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.450 AC: 68074 AN: 151180 Hom.: 15562 Cov.: 29 AF XY: 0.446 AC XY: 32913 AN XY: 73754

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.498

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.470

Alfa AF: 0.449 Hom.: 21251

Bravo AF: 0.464

Asia WGS AF: 0.419 AC: 1456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.61

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7173743; hg19: chr15-79141784;